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GregoryFaust / samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
MIT License
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More info for missing pair #22

Closed zeeev closed 8 years ago

zeeev commented 8 years ago

@GregoryFaust ,

I'm trying to track down a problem with grouping reads. The error I get:

samblaster: Can't find first and/or second of pair in sam block of length 1 for id: xxxxx

It would be exceptionally helpful if the error reported the chromosome and position of the read so they could be quickly pulled for examination.

Thank you.

GregoryFaust commented 8 years ago

Closed in release 0.1.23

jiadong324 commented 8 years ago

@GregoryFaust Dear author,

I have the same issue here. But what do you mean by "Closed in release 0.1.23"? I am using 0.1.23 right now. And I am using "samtools sort -n" command to sort bwa aligned reads in a SAM file.

What do you think of it? Thanks in advance!

vyx-greg-faust commented 8 years ago

By "Closed in 0.1.23" I mean that I included the requested additional information into the error message for missing mate, namely the chromosome and position of the read that produced the error.

Yes, "samtools sort -n -O SAM" or "sambamba sort -n -u -o /dev/stdout | sambamba view -f sam -h" will work to sort output from bwa or any other paired-end read aligner in a way that samblaster can use.

jiadong324 commented 8 years ago

@vyx-greg-faust Thanks for your explanation and instructions.